On 18 April 2014 14:59, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary <saketkc@gmail.com> wrote:
John pointed out that the error its the upload of the test file itself which is failing. I can locate the input files in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530 This happens irrespective of using ftype. and the plce where ERROR occurs is this: galaxy.jobs.runners.local DEBUG 2014-04-17 21:25:53,808 execution finished: GALAXY_SLOTS="1"; export GALAXY_SLOTS; python /home/travis/build/saketkc/galaxy_tools/galaxy-central-master/tools/data_source/upload.py /home/travis/build/saketkc/galaxy_tools/galaxy-central-master /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpv9tzOU 1:/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/dataset_1_files:/tmp/tmpNenHnc/tmp83XrmN/database/files/000/dataset_1.dat galaxy.datatypes.metadata INFO 2014-04-17 21:25:55,902 /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn galaxy.jobs.runners DEBUG 2014-04-17 21:25:55,903 executing external set_meta script for job 1: /home/travis/build/saketkc/galaxy_tools/galaxy-central-master/set_metadata.sh /tmp/tmpNenHnc/tmp83XrmN/database/files /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1 . /tmp/tmpNenHnc/functional_tests_wsgi.ini /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/galaxy.json /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn galaxy.jobs.runners DEBUG 2014-04-17 21:25:57,620 execution of external set_meta for job 1 finished galaxy.jobs DEBUG 2014-04-17 21:25:57,727 setting dataset state to ERROR so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
Likely unrelated, but I don't think I have bothered to set the ftype when uploading tabular files / using them as test inputs. Did you ever try this without the ftype?
Peter